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1answer
32 views

How to compute the mean 2D slice of a 3D set of data in MPI

I have a 3D set of data v(i,j,k), and I want to compute the mean 2D slice vmean(i,j) summing up the ...
1
vote
1answer
49 views

Dealing with boundary conditions using Fourier spectral methods

I am currently working on a project where I need to use Fourier spectral methods to solve the KS equation. I found this code which is using the Fourier spectral methods to solve the classic 1D heat ...
-4
votes
1answer
47 views

How do I graph this in python? [closed]

$$ y=\cases{-\sqrt{|x|}, \quad x\le0\\\sqrt{x}, \quad x>0} $$ I've tried graphing this in python, but can't seem to figure it out. Does anyone know how to do this by chance?
0
votes
1answer
52 views

Retaining or mapping sets (physical tags) after remeshing a compounded surface/curve in Gmsh?

For my current work, I need to remesh a given geometry with Gmsh (currently trying all Gmsh versions to achieve this) to continue my Abaqus simulations. As can be seen in the image, the geometry has ...
6
votes
1answer
89 views

Is there any theory of the minimum amount of data for tomographic reconstruction?

I'm doing an experiment on synthetic data and I want to generate enough data but not too much. So I wonder if there is any rule for the minimum number of projection angles and detector count. For ...
1
vote
0answers
53 views

How to minimize a integral function using a constant step gradient method in Python?

I am developing a practical work of the following system of ode \begin{align}x'(t) &= k_1h(t) - (k_2+k_3)x(t)\\ y'(t) &= k_3x(t)\end{align} and $z(t) = (1-k_4)(x(t)+y(t))+k_4h(t)$, where $h(...
2
votes
2answers
78 views

Packing spheres inside a geometry

I am looking for packing spheres (can be monodisperse or polydisperse with known radii distribtuions) inside a geometry. I am sure this is a well explored scientific problem with applications in ...
2
votes
0answers
64 views

Correct approach for thermal finite element simulation of layered assembly

I would like to optimise the heat transfer on a PCB. Several dies are on the top and cooling air is going through the fins in heat sink on the bottom. The assembly consists of several layers like ...
3
votes
1answer
176 views

log-sum-exp trick for signed/complex numbers

I need to evaluate a sum of values that are on many different orders of magnitude in scale but might be signed. I’ve had great luck with the “log-sum-exp” trick for an unsigned version of my problem, ...
0
votes
0answers
18 views

How to use the solution of a multistage stochastic program?

Given a multistage stochastic program, its solution (if it exists) consists of the first decision vector, as well as all the recourse decision vectors for all possible scenarios of an event tree. But ...
2
votes
0answers
26 views

2-dimensional Gauss-Hermite quadrature in R

A similar question was asked here and the given answer is perfect for a unidimensional integration. I need to make bidimensional integration in R with a Gauss-Hermite quadrature: $$\int_{R^2} h(p1,p2)...
0
votes
0answers
61 views

A name for a numerical phenomena when using numerical methods

I have a nonlinear solver for equation $g= c_1f(x_1,y_1)+c_2f(x_2,y_2)$. Note that $c_1$ is much bigger than $c_2$. So after using Levenberg–Marquardt algorithm, I could only get $x_1$, $y_1$ and $...
1
vote
1answer
44 views

Filling a volume with generalised polyhedra

Given a volume (say, some polyhedron), I need to fill it with smaller polyhedra, such that the space is filled as much as possible. The constraints and relaxations are: (0) For a computation ...
1
vote
1answer
118 views

Application of Poiseuille equation

I'd like to know whether the Hagen-Poiseuille equation can be used to solve for the velocity of fluid when the Reynolds number (Re) is less than 1. From textbooks, I understand that the Hagen-...
4
votes
0answers
122 views

Explanation of subspace strategy regarding CG described in Golub's book

I was wondering about the last paragraph in Matrix Computations (4th edition) by Golub, Chapter 11 (11.3.3), specifically his explanation of subspace strategy for Conjugate Gradient. Note that in ...
-1
votes
3answers
153 views

Solving coupled ODEs using Runge-Kutta method

I want to solve the following sets of $n$ coupled equations. Initial values of $x_{n}(t)$ and $p_{n}(t)$ are specified. The problem is, I have an 1D lattice where every particle is bound with ...
0
votes
0answers
39 views

Propagation of a Gaussian beam using FFT

I am trying to simulate the propagation of a gaussian beam through a lens using an FFT approach. I tried to implement the approach described by Couairon in this paper at page 43: https://link....
4
votes
2answers
2k views
1
vote
1answer
71 views

How to choose between compact finite differences and spectral methods

For a project in my advanced numerical method class I have to solve the 1D Kuramoto-Sivashinsky equation. $$ u_t + u u_x + \lambda u_{xx} + \eta u_{xxxx} = 0. $$ As explained here I will solve it ...
0
votes
0answers
32 views

How to implement the gmres method using Householder transformation instead of the Gram-Schmidt?

For Generalized Minimal Residual method GMRES, we usually use the Modified Gram-Schmidt MGS to generate an orthonormal basis of ...
1
vote
1answer
61 views

Type of Rosenbrock method by its coefficients

A Fortran code that solves stiff PDE systems contains the following arrays of Rosenbrock-Wanner method coefficients: ...
7
votes
1answer
166 views

evaluating $\coth(x) - 1/x$ for real $x$, on 2 “pieces”

The function $\coth(x) - 1/x$ has a removable singularity at 0. Its Taylor series is: $$ \coth(x) - 1/x = \frac{x}{3} - \frac{x^3}{45} + \frac{2x^5}{945} + \ldots $$ I would like to evaluate the ...
1
vote
2answers
65 views

Why Householder transformation can not be chosen to be an identity matrix?

For Householder transformation, we know that $H = I-uu^T$, where $\|u\|_2=\sqrt{2}$. When it acts on any vector $x$, $Hx$ and $x$ is symmetric with respect to $span(u)^T$. But I have read a ...
1
vote
1answer
48 views

Initial condition for Kuramoto-Sivashinsky

For a project in my advanced numerical method class I have to solve the 1D Kuramoto-Sivashinsky equation of which I know little. I just know that it was derived the equation to model the diffusive ...
3
votes
0answers
53 views

Solving saddle point problem having non-invertible top-left block with a PETSc nested matrix

My system is a symmetric FE problem with lagrange multipliers: $Z=\begin{pmatrix}A & C^T \\ C & 0\end{pmatrix}$ The matrix $A$ is positive semi-definite, non-invertible. The whole matrix is ...
3
votes
0answers
38 views

Hit-n-Run Monte Carlo on convex polytope

So, I'm currently trying to implement a MCMC to uniformly sampling hyper-points from the polytope defined as $\mathbb{K}=\{x\in\mathbb{R}^{n}\;\;\text{s.t.}\;\; A\,x=b \}$ in the specific case where, ...
2
votes
1answer
133 views

Efficient ways to numerically evaluate matrix exponentials

What are some computationally efficient ways to solve matrix exponentials, i.e. functions of the form : f(X)=$e^{X}$, where X is a square matrix ? So far I have been able to diagonalise some ...
1
vote
1answer
55 views

Using adolc for the sign function in c++

Here is an implementation of the sign function in C++ using Adolc librairy for automatic differentiation. ...
1
vote
1answer
35 views

Determinant of a matrix after removing or adding lines and columns

In quantum mechanics, the wavefunction of N electrons is given by a determinant. I am working on a Monte Carlo algorithm. At each Monte Carlo step, I need to add or remove an electron, which means ...
2
votes
2answers
153 views

Inverting really big symmetric block diagonal matrix

I have a really big symmetric 7.000.000 X 7.000.000 matrix that i would like to invert. The matrix is extremely sparse and it can be rearranged as to become a block diagonal matrix. The biggest blocks ...
4
votes
0answers
57 views

Why the two Gram-Schmidt algorithms produce different results for qr factorization?

For the qr factorization using classic Gram-Schmidt algorithm, I found the 2 different implementations below. The first one uses the for loop to compute the upper ...
2
votes
1answer
54 views

pdepe or Crank-Nicolson? How much is pdepe good?

I am beginner in MATLAB and similar. I sow and discussed with my professors doing simulations some times: they wrote down a lot of calculus, most of them using Crank-Nicolson Method and so implement ...
1
vote
2answers
204 views

How to simulate over 1 billion particles?

I want to simulate human erythrocytes in capillaries. I calculated, that for a 1 meter long and 1 mm in diameter capillary there are about 3 billion blood cells. Erythrocytes are actually discs, but ...
4
votes
1answer
71 views

Why the solid FEM problem can not be solved after constraining 3 degrees of freedom?

I write a simple MATLAB code for solving solid FEM problem. The problem looks like that (1) (2) x-------x | / | | / | | / | x-------x (3) (4) ...
32
votes
2answers
11k views

why is A*v+B*v faster than (A+B)*v?

$A$ and $B$ are $n \times n$ matrices and $v$ is a vector with $n$ elements. $Av$ has $\approx 2n^2$ flops and $A+B$ has $n^2$ flops. Following this logic, $(A+B)v$ should be faster than $Av+Bv$. Yet,...
1
vote
2answers
89 views

Is the similar subdivision of a delaunay mesh still delaunay?

I have a delaunay triangulation for a 2d box with say an airfoil inside. If I uniformly refine this mesh by subdividing each triangle in the mesh into 4 triangles by halving each edge, is the ...
0
votes
0answers
53 views

Is it possble to do this complex symbolic calculation with Matlab?

Sorry it's bit abrupt, but recently I am caught up in some symbolic calcualtion which is tedious and almost impossible with mere human hands, so just wondering is it possible to solve the double ...
12
votes
4answers
720 views

Example where autodiff works but symbolic differentiation will not?

According to the survey paper on autodiff (linked) Autodiff works on inputs that cannot be specified in closed form but can be described by a sequence of code, each component of which is ...
4
votes
1answer
116 views

Computation of triple nested loops as a convolution product?

I'm trying to compute efficiently the following \begin{equation} A_j = \sum_{l'=1}^{\infty}\sum_{k= 0}^{K-1} L_{l'}T_ke^{2\pi i \frac{k}{K}j}\epsilon_{l',k} \end{equation} for $j = 0,1, \ldots, K-2,K-...
1
vote
0answers
58 views

Can Representation Theory be studied computationally / numerically?

Can a subfield such as the representation theory of Lie algebras be studied computationally / numerically -- is there an interplay between the abstract and the concrete? I would be grateful for an ...
2
votes
1answer
57 views

Solution method of nonlinear heat transfer analysis

The governing equation of transient heat transfer analysis is described as follows: $$C \frac{dT}{dt}+K T = Q$$ When using backward difference scheme for the discretization of the time we get the ...
1
vote
2answers
166 views

How to vectorize 2 nested for loop with one complex condition in the inner loop?

Octave calculations is too slow specially when you deal with scientific calculations that can span a very very large matrix, even just iterating. I have to vectorize it to speed up the calculation. ...
2
votes
1answer
91 views

Is this a valid way to implement Neumann BCs in finite differences?

I'm trying to solve the 1D heat equation with Neumann boundry conditions numerically using finite differences: $$u_t = \alpha u_{xx}$$ $$u_{x}(0, t) = u_{x}(L, t) = k$$ $$u(x, 0) = u_0(x)$$ The main ...
0
votes
2answers
45 views

contour plot of cloud of points [closed]

I have a cloud of points scattered in a rectangle and some data in this points, a bit like this $$ x(:)=[x(1), x(2), ..., x(N)] \\ y(:)=[y(1), y(2), ..., y(N)] \\ u(:)=[u(1), u(2), ..., u(N)] $$ ...
4
votes
0answers
89 views

Trying to understand splitting-based iterative method for 2D Laplace problem

I am trying to understand the theory behind a splitting based iterative method which uses the incomplete Cholesky factorization. Before giving the specific details, let me first give the problem ...
2
votes
0answers
40 views

Avoid matrix multiplication in algebraic multigrid method

Currently when I try to solve a linear algebra system of the form of $A x =b$ I use the algebraic multigrid method. The algebraic multigrid method uses a Galerkin product to form the coarse grid ...
3
votes
1answer
86 views

Can one publish a new model and simulation without physical experiments?

When I read strong papers from, say, the Journal of Fluid Mechanics, a simple model, simulations and physical experimental results are given, showing good agreement. Can one publish a new model and ...
3
votes
1answer
106 views

Calculation of Mean Square Displacement for Brownian dynamics system with Lennard Jones interactions in python3

I have a problem getting a sensible result for the Mean Square Displacement (MSD) for a simulation of $N$ particles under Brownian dynamics with Lennard-Jones interaction between them with or without ...
3
votes
0answers
35 views

Integer partition algorithms

I am familiar with and have written MathCad algorithms for the partition functions 𝑝(𝑛,𝑘),which gives the number of ways of partitioning 𝑛 into 𝑘 parts, 𝑞(𝑛,𝑘), which gives the number of ways ...
3
votes
0answers
51 views

Levinson Recursion for Non Square Toeplitz Matrices

Given a rectangular Toeplitz Matrix $ H $, how could one solve: $$ y = H x $$ For instance, $ H $ can be Linear Convolution Matrix of the filter $ h $: $$ H = \begin{bmatrix} {h}_{1} & 0 & ...

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